[gmx-users] Unnatural amino acid MD

Ashutosh Jogalekar ajogale at emory.edu
Mon Mar 6 18:22:55 CET 2006

I am trying to do MD on a peptide with an unnatural amino acid, and i  
have duly modified the OPLS forcefield .hdb, .rtp, and aminoacid.dat  
file accordingly. Now, when I am trying to do the grompp for the  
energy minimization, the program is asking me to put parameters for  
the dihedrals in the .top file. I did put most of them in, but cannot  
find values for the other ones. More importantly, some of the  
dihedrals don't make sense, because they don't seem to have anything  
to do with keeping an aromatic ring flat, for example. A few improper  
dihedrals should suffice for my amino acid, which is phenylglycine.  
But the ones that the program is asking me to put in seem to  
correspond to quite obscure atom combinations. Is this a problem with  
gromacs, or with the OPLS force field that I am using?
Ashutosh Jogalekar
Emory University

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